CHip-Seq

Chromatin Immunoprecipitation is an important molecular tool used to discover all parts of the genome that a transcription factor can bind to. Chromatin Immunoprecipitation, or CHip-Seq, involves the use of antibodies that bind to the transcription factor of choice in order to withdraw all the genetic material from the cells. The first step requires the crosslinking of proteins and DNA together. Once the Transcription factor has been attached to the DNA, the DNA is sheared into 300 base pair segments. Next beads with antibodies that recognize a specific transcription factor are added so that the DNA-transcription factor complex binds to it. The immunoprecipitation part of this experiment involves centrifuging the substance so that a pellet is formed containing only the beads that are attached to the DNA-transcription factor complex. The protein is then uncrosslinked from the DNA and the short strands now get sequenced. The sequenced DNA portions are then mapped on the genome to see where the transcription factors bind. This experiment can reveal valuable information when combined with RNA-Seq. RNA-Seq will give all the genes that are acitive so overlapping the results of a CHip-Seq test will tell you what genes are activated by a specific transcription factor.